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v1.7.9 Release

· 2 min read

We are pleased to present v1.7.9!

This release features several bugfixes and improvements submitted by community members, including a CLI fix when specifying --indexFile with CSI files, and a new feature to get FASTA metadata from an external file.

Additionally, we have switched to canvas2svg for SVG exports, which can now handle more sophisticated operations like bezierCurves (used for sashimi-style arc in RNA-seq data), and circles (used by jbrowse-plugin-gwas)

Before (note bad intron and lack of arcs rendered on bottom track)

After (fixed intron rendering and arcs)

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.7.9 (2022-06-02)​

🚀 Enhancement​

  • core
    • #2991 Use canvas2svg for SVG export, fixes non-rasterized usage of bezier, arcs, and more (@cmdcolin)
    • #2483 Add setting to color by query score per alignment for dotplot, support HTML in config slot descriptions (@cmdcolin)
    • #2983 Set target=_blank by default in user HTML links (@cmdcolin)
  • Other

🐛 Bug Fix​

  • core
  • Other
    • #2977 Respect --indexFile option when adding VCF and BED tracks (@heavywatal)
    • #2974 Fix track indexing being ignored after first add track widget usage (@teresam856)

🏠 Internal​

Committers: 4​

v1.7.8 Release

· 2 min read

We are happy to announce v1.7.8

Some highlights include

  • ~20% speed improvement for CRAM data
  • bugfix for filter-by being broken on alignments tracks in v1.7.0-v1.7.7
  • bugfix for certain methylation/modifications being drawn incorrectly on alignments tracks
  • bugfix for the "Open" button not navigating to the correct location on the LGV import form
  • improved visualization of indels in methylation/modifications mode on alignments tracks
  • skip text index query if the input is a loc string, resulting in quicker navigation

Screenshots showing the new viewing of indels when viewing methylation

Before

After

See the release notes for details

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.7.8 (2022-05-20)​

🚀 Enhancement​

🐛 Bug Fix​

  • #2969 Fix link on yeast synteny demo and fix CIGAR rendering on dotplot (@cmdcolin)
  • #2964 Fix crash displaying modifications called on softclipped regions of reads (@cmdcolin)
  • #2965 Fix filter functionality on pileup tracks (@cmdcolin)
  • #2953 Fix "Open" button on LGV ImportForm (@cmdcolin)
  • #2952 Fix read vs ref not finding primary alignment on certain CRAM files (@cmdcolin)
  • #2951 Fix viewing soft/hardclip indicator in some regions (@cmdcolin)

📝 Documentation​

🏠 Internal​

Committers: 2​

v1.7.7 Release

· One min read

This is a small bugfix release, where in v1.7.5-1.7.6 the read vs ref and sequence panels in the feature details failed to load

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.7.7 (2022-05-04)​

🐛 Bug Fix​

🏠 Internal​

  • core
    • #2944 Avoid stalling on undefined assemblyName during ref name renaming (@cmdcolin)

Committers: 1​

v1.7.6 Release

· One min read

This fixes a bug that affected v1.7.0-v1.7.5 in which CRAM, TwoBit, and other file types would not load on jbrowse-desktop. This was due to the upgrade to webpack 5/CRA5, but is fixed in this release!

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.7.6 (2022-04-26)​

🐛 Bug Fix​

  • #2939 Fix loading CRAM, TwoBit, and other modules that use @gmod/binary-parser on jbrowse desktop (@cmdcolin)

Committers: 1​

v1.7.5 Release

· 2 min read

We are pleased to present the release of v1.7.5

This release includes two major improvements

  • Ability to index tracks for searching by gene names in JBrowse Desktop. This let's users choose per-track indexes in the add track widget interactively, or index them after-the-fact using the track menu.
  • Removed serialization of BAM/CRAM features for pileup tracks which brings large performance benefits for jbrowse-web and jbrowse-desktop. Previously, all the BAM/CRAM features were serialized across the RPC boundary in jbrowse-web and jbrowse-desktop, but this was an expensive and memory intensive operation. Now, the BAM/CRAM features are not serialized, but the main thread has to manually request any data it needs from the worker after rendering (e.g. when we click a feature).

Figure showing the "Index track" option in the track menu of JBrowse Desktop

Figure showing the "Index track" option in the add track widget of JBrowse Desktop

Figure showing performance improvement of the noserialize improvement compared with v1.7.4, which brings the webworker performance in line with the embedded app (which does no serialization)

This release also fixes a bug with using trix indexes created by jbrowse text-index in v1.7.0-v1.7.4 (with the adjustable prefix size)

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.7.5 (2022-04-26)​

🚀 Enhancement​

  • core
    • #2885 Reduce serialization overhead on alignments tracks and access feature details asynchronously (@cmdcolin)
  • Other
    • #2935 Use the name "Read Sequence" for the read vs ref view (@cmdcolin)
    • #2916 Add vite setup to our embedded component demos (@cmdcolin)
    • #2927 Optimize gtf by only parsing lazily per-refName (@cmdcolin)
    • #2928 Add vanillajs/script tag loading embedded components demos (@cmdcolin)
  • core, text-indexing

🐛 Bug Fix​

  • #2863 Render gene with CDS subfeatures properly (@cmdcolin)
  • #2934 Bump @gmod/trix to fix prefix size calculation and searching first word in index (@cmdcolin)

Committers: 3​

v1.7.4 Release

· One min read

This is a small patch release that fixes our UMD builds for embedded components fixes the @babel/runtime dependency in some npm packages

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.7.4 (2022-04-19)​

🐛 Bug Fix​

Committers: 2​

v1.7.0 Release

· 3 min read

We are excited to announce the latest JBrowse release! This has many great features including

  1. Floating feature labels, so if you are zoomed into the middle of a gene, the feature label hangs out alongside it on the left side of the screen! The results may not be pixel perfect in all cases (reverse complement labels can end up overlapping other features for example) but we hope this helps you see the labels for features that extend off the screen!

    Figure showing the feature labels floating alongside gene even when you are zoomed into the feature

  2. Upgraded build system for jbrowse-web and jbrowse-desktop to webpack 5, and added examples of using webpack 5 with embedded components. Webpack 5 results in smaller build sizes for jbrowse-web. For a typical session, amount of .js downloaded with gzip enabled in v1.6.9 is ~1.4MB, in v1.7.0 ~900kb (-500kb smaller). Without gzip enabled v1.6.9 4.8MB, v1.7.0 2.5MB (-2MB smaller). The result is largely due to better webworker bundling. See https://jbrowse.org/jb2/docs/embedded_components/ for webpack 5 examples in embedded components

  3. Optimizations and improved visualization of paired-end reads in the breakpoint split view

  4. Optimized linear synteny renderings with long CIGAR strings. These optimizations help viewing large alignments such as the CHM13-T2T-v2.0 assembly vs hg38 PAF file from https://github.com/marbl/CHM13#downloads (example here https://jbrowse.org/code/jb2/main/?config=test_data%2Fconfig_demo.json&session=share-0qD2-d_k4K&password=GF8Sk)

  5. The "Assembly selector" dropdown box now remembers your last selection, so you can more easily return to your genome of interest

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.7.0 (2022-04-14)​

🚀 Enhancement​

  • Other
    • #2909 Add --prefixSize flag to @jbrowse/cli text-index (@cmdcolin)
    • #2887 Optimize filtering on alignments tracks (@cmdcolin)
    • #2879 Multi-level synteny rubberband (@cmdcolin)
    • #2874 Optimizations for rendering long syntenic alignments e.g. CHM13 vs GRCh38 (@cmdcolin)
    • #2872 Better connection between paired-end alignments in breakpoint split view and optimizations (@cmdcolin)
  • core
    • #2902 Standardize heights of widgets in LGV import form (@cmdcolin)
    • #2781 Add floating labels to SVG features (@cmdcolin)
    • #2875 Make assembly selector remember your last selected assembly (@cmdcolin)
    • #2860 Avoid performing many peekTransferables to optimize RPC serialization (@rbuels)

🐛 Bug Fix​

  • Other
    • #2908 Fix AboutDialog under vite for embedded components (@cmdcolin)
    • #2900 Fix the 'Open assembly' menu item in jbrowse desktop (@cmdcolin)
    • #2882 Add padding at the bottom of the configuration editor to help color editing popup being cutoff (@cmdcolin)
    • #2877 Fix strand on arrows in horizontally flipped mode (@cmdcolin)
  • core
    • #2891 Use a user-supplied fetchESM callback to import ESM plugins to fix 'Critical dependency...' errors from embedded components (@cmdcolin)

📝 Documentation​

🏠 Internal​

  • core
    • #2904 Use a user-supplied fetchCJS callback to import CJS plugins (@cmdcolin)
    • #2891 Use a user-supplied fetchESM callback to import ESM plugins to fix 'Critical dependency...' errors from embedded components (@cmdcolin)
    • #2857 Refactor and improve types of OffscreenCanvas shim and ponyfill (@rbuels)
  • __mocks__, core

Committers: 3​

v1.6.9 Release

· One min read

This is a re-release of 1.6.8 to fix the Mac build of JBrowse Desktop

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

v1.6.8 Release

· 2 min read

We are pleased to announce the v1.6.8 release!

This release includes a change to the default gene style to use boxes instead of "chevron" features, with a directional arrowhead

Before

After

Some additional highlights

  • Draws the correct the proportion of SNPs when displaying the SNPCoverage height in log scale (thanks @gringer for reporting)
  • Adds more optimizations for some alignments tracks
  • Adds a per-base drawing mode to alignments tracks

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.6.8 (2022-03-25)​

🚀 Enhancement​

🐛 Bug Fix​

  • Other
    • #2852 Fix misaligned features under breakpoint split view (@cmdcolin)
    • #2844 Fix layout of small features without labels for SvgFeatureRenderer (@cmdcolin)
    • #2839 Fix the drawing of SNP height when the SNPCoverage track is using log scale (@cmdcolin)
    • #2825 Fix tracklabels positioning not updating in UI after user selection (@cmdcolin)
  • core

Committers: 3​